Late last month the National Center for Biotechnology Information, or NCBI, released a new resource containing information on genetic tests. The resource’s name is the Genetic Testing Registry (GTR), and according to its homepage, the GTR:
” provides a central location for voluntary submission of genetic test information by providers. The scope includes the test’s purpose, methodology, validity, evidence of the test’s usefulness, and laboratory contacts and credentials. The overarching goal of the GTR is to advance the public health and research into the genetic basis of health and disease.”
I’m always interested in checking out new resources from NCBI, especially when it is my turn to do a weekly tip. Initially I figured that I would check out the GTR and post a video on how to use it – but the NCBI beat me to that. You can see their YouTube tips (there are two) by clicking the link on their homepage & learn some search tips, etc. [Note, the two videos continued to loop for me & I needed to stop them after viewing them once].
But the question that I came up with is, “What will the GTR provide me with that I am not already getting from other clinical resources that I use, and that OpenHelix trains on?” I try to address that question in my video by doing the same search, for “Cystic fibrosis”, at five different clinically-related resources, and discussing what each offers and specializes in doing. Of course, in a five minute video I can’t be comprehensive – either for resources or what they cover – but I think it will give you enough of a taste for you to appreciate what the GTR offers you, or to continue the comparison on your own.
The resources that I visit in the tip movie are: the GTR, GeneTests, the Genetic Home Reference (GHR), OMIM, and Orphanet. At each resource I do a basic search for the the disease “Cystic fibrosis” and show the initial results display that resulted. I don’t have time to compare the detailed reports available at each, but lower on the post I link to a reference on the resource (if available), as well as the landing page for OpenHelix training materials on the resource – since we have a tutorial on many of these resources. I also include direct links to each resource.
I’d suggest that you read the NIH News article on the GTR release for some background on the GTR. I won’t cover everything here, but there are a couple of paragraphs that I want to point your attention to. The first explains the relationship between GeneTests and GTR, and says:
“GTR is built upon data pulled from the laboratory directory of GeneTests, a pioneering NIH-funded resource that will be phased out over the coming year. GTR is designed to contain more detailed information than its predecessor, as well as to encompass a much broader range of testing approaches, such as complex tests for genetic variations associated with common diseases and with differing responses to drugs. GeneReviews, which is the section of GeneTests that contains peer-reviewed, clinical descriptions of more than 500 conditions, is also now available through GTR.”
It seems to be another case where it was deemed easier to start a new resource (GTR) than to try and revamp an old resource (GeneTests) to handle the amazing influx of new data. Often resources aren’t retired as soon as expected, due to user feedback, but it is important to note that GTR seems to be in place to eventually replace GeneTests. I assume the GeneReviews will still be edited by & copyright to the University of Washington, Seattle, but I don’t have a reference for that. The similar transition occurred for OMIM, which was hosted at NCBI for years but now has a new URL at Johns Hopkins (watch for our new tutorial on OMIM, which is currently in the works).
The second paragraph that I found particularly interesting was the one on what the GTR contains, and will contain. It states:
“In addition to basic facts, GTR will offer detailed information on analytic validity, which assesses how accurately and reliably the test measures the genetic target; clinical validity, which assesses how consistently and accurately the test detects or predicts the outcome of interest; and information relating to the test’s clinical utility, or how likely the test is to improve patient outcomes.”
I didn’t immediately find mention of who will provide the validity or utility information in the GTR documentation, which is currently under construction. It is clear that much of the content of the database will be “voluntarily submitted by test providers”, and it is stated that “NIH does not independently verify information submitted to the GTR; it relies on submitters to provide information that is accurate and not misleading.”, but I also saw that experts will input on GTR’s content regularly, as can be read here. The GTR team is also very interested in receiving input on the resource, which can be submitted through the GTR feedback form.
The Genetic Testing Registry (GTR) – http://www.ncbi.nlm.nih.gov/gtr/
GTR YouTube Tips from NCBI – http://www.youtube.com/playlist?list=PL1C4A2AFF811F6F0B
GeneTests Introductory Tutorial by OpenHelix* – http://bit.ly/genetests
Genetic Home Reference (GHR) – http://ghr.nlm.nih.gov/
GHR Introductory Tutorial by OpenHelix* – http://bit.ly/geneticshomeref
Online Mendelian Inheritance in Man (OMIM) – http://www.omim.org/
OMIM Introductory Tutorial by OpenHelix – (coming soon, currently being updated)
Orphanet – http://www.orpha.net/
*OpenHelix tutorials for these resources available for individual purchase or through a subscription
For GeneTests (free from PMC) – Pagon RA (2006). GeneTests: an online genetic information resource for health care providers. Journal of the Medical Library Association : JMLA, 94 (3), 343-8 PMID: 16888670
For GHR (free from PMC) – Mitchell JA, Fomous C, & Fun J (2006). Challenges and strategies of the Genetics Home Reference. Journal of the Medical Library Association : JMLA, 94 (3), 336-42 PMID: 16888669
For OMIM (open access article) – Amberger, J., Bocchini, C., & Hamosh, A. (2011). A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) Human Mutation, 32 (5), 564-567 DOI: 10.1002/humu.21466
For Orphanet (full access requires subscription) - Aymé, S., & Schmidtke, J. (2007). Networking for rare diseases: a necessity for Europe Bundesgesundheitsblatt – Gesundheitsforschung – Gesundheitsschutz, 50 (12), 1477-1483 DOI: 10.1007/s00103-007-0381-9